title: Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing.
abstract: BACKGROUND
  Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes.
  
  
  RESULTS
  We now report a much deeper analysis using the SOLiD™ technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation.
  
  
  CONCLUSIONS
  This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes.
authors.affiliation: Structural & genomic Information Laboratory (CNRS, UPR2589), Mediterranean Institute of Microbiology, Aix-Marseille Université, 163 Avenue de Luminy, Case 934, FR-13288 Marseille, France. matthieu.legendre@igs.cnrs-mrs.fr
authors.forename: Matthieu
authors.initials: M
authors.lastname: Legendre
authors.forename: Sébastien
authors.initials: S
authors.lastname: Santini
authors.forename: Alain
authors.initials: A
authors.lastname: Rico
authors.forename: Chantal
authors.initials: C
authors.lastname: Abergel
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
mesh_terms: D000595:Amino Acid Sequence; D020869:Gene Expression Profiling; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D056686:Mimiviridae / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins